CHANGES

version 4.5.22
- fixed 'fg.col' and 'bg.col' handling in 'tile'

version 4.5.21
- set 'col = "white"' for grid lines in 'displayRaster'

version 4.5.20
- added grid lines to 'displayRaster'
- cleaned up 'displayRaster' code

version 4.5.19
- 'displayRaster' does not restore 'par' graphical parameters on exit
- fixed 'interpolate' argument passing in 'displayRaster'

version 4.5.18
- improvements to documentation

version 4.5.17
- added 'luminance' conversion mode to 'channel'
- removed old code of 'writeImage'
- added package news from previous versions to 'NEWS.Rd'
- updated CHANGES

version 4.5.16
- further memory and performance improvements to 'readImage'
- 'clipImage' now relies on the C coded 'normalize' function (up to 5x faster!)
- significant performance improvements (up to 2x faster):
  'Image'
  'is.Image'
  'selectChannel'
  'show'
  'flip'/'flop'
- minor performance improvements (i.e. by using call to 'new' instead of 'Image'):
  'validImage'
  'filter2'
  'colorLabels'
  'rgbImage'
  'affine'
  'tile'
  'isXbitImage'
  'writeImage'
- when called on an Image object 'as.Image' returns now it's argument rather than the Grayscale-coerced copy
- Image constructor handles now properly multi-dimensional character arrays
- fixed color mode check in 'validImageObject'
- removed unnecessary calls to 'validObject'
  NOTE: there is no need to check for object validity after creating it with 'new' (this is done automatically by R)
- added some missing imports from 'methods' to the NAMESPACE file

version 4.5.15
- memory improvement to 'readImage'

version 4.5.14
- minor improvements to 'is.Image' and 'transpose'

version 4.5.12
- updated man page of 'flip', 'flop', and 'rotate'

version 4.5.11
- fix to 'getFrame' and 'combine' for single channel Color Images
- added convenience function 'toRGB'

version 4.5.10
- fixed performance of 'readImage', especially on big image stacks

version 4.5.9
- 'colorLabels' now supports multidimensional images

version 4.5.8
- 'getFrame' now uses 'asub' from the abind package

version 4.5.7
- improved code and performance of 'colorLabels'

version 4.5.6
- updated 'getNumberOfFrames' and 'getFrame' functions to support multi-dimensional images

version 4.5.5
- added 'interpolate' parameter to the internal 'displayRaster' function

version 4.5.4
- fixed header title in the vignette
- rolled back the change from 'array' to 'as.array' from previous commit

version 4.5.3
performance optimizations:
- changed 'array' call to 'as.array' in Image constructor
- 'normalize' does not reassign returned value to the original object

version 4.5.2
- minor modifications to code and documentation

version 4.5.1
- moved vignette from 'inst/doc/' to 'vignettes/'

version 4.3.7
- fixed a bug in 'getFrame' function: XY dimensions equal 1 were dropped

version 4.3.5
- minor documentation fixes

version 4.3.4
- modified the 'normalize' function to accept presetting the input intensity range (requested by Bernd Fischer)
- added 'colorLabels' function by Bernd Fischer

version 4.3.3
- vignette uses now the 'BiocStyle' formatting

version 4.3.2
- 'normalize' now uses the generic from BiocGenerics

version 4.3.1
- fixed the redefinition of default arguments in C function templates which triggered errors in the clang compiler

version 4.1.7
- updated 'NEWS.Rd' and vignette papersize

version 4.1.6
- fixed long argument handling in 'deparse()' by adding 'width.cutoff' and 'nlines'
- changed brush size in the 'morphology.Rd' from 100 to 99
- maintainer changed

version 4.1.5
- fixed a bug in the 'medianFilter' function caused by incorrect [0:1] <> integer range conversion

version 4.1.4
- fixed a bug in the 'erode'/'dilate' functions introduced by the previous fix in version 3.99.2

version 4.1.3
- added function 'localCurvature' to compute local signed curvature along a line segment

version 4.1.2
- fixed a bug in the 'resize' function causing the new image width to be calculated incorrectly when only height was provided (reported by Bernd Fischer)
- the range of pixel coordinates displayed in the Javascript viewer is now (1,1):(w,h) rather than (0,0):(w-1,h-1) and matches the indices of the corresponding Image array

version 4.1.1
- "inline double peekpixel" has been changed to "static inline double peekpixel", to be C99 compatible (thanks to Nathan Coulter)

version 3.99.19
- improved JavaScript image viewer with some minor bugs fixed
- removed unused files from 'scripts/'
- added 'NEWS.Rd'

version 3.99.18
- further improvements to the JavaScript image viewer; exit on-screen help using either 'ESC' or 'Q'
- added 'transpose' to unit tests

version 3.99.17:
- removed all dependencies towards GTK+ and ImageMagick
- deprecated: blur, equalize,
- deprecated: drawtext, drawfont
- deprecated: getFeatures, hullFeatures, zernikeMoments, edgeProfile, edgeFeatures
- deprecated: haralickFeatures, haralickMatrix
- deprecated: moments, smoments, rmoments, cmoments
- overhauled the testing procedure in tests/test.R

version 3.99.16
- CSS fix disabling bilinear filtering of rescaled images in the JavaScript image viewer

version 3.99.15
- numerous improvements and bug fixes to the JavaScript image viewer, including: on-screen help displayed by pressing 'H', and fixed mouse wheel action (now consistent behavior across browsers and platforms)

version 3.99.14
- minor documentation updates

version 3.99.13
- improved JavaScript image viewer with upgraded user interface

version 3.99.12
- renamed 'swapXY' to 'transpose'
- updated documentation on 'transpose', 'readImage', writeImage', and 'display'

version 3.99.11
- better argument handling in the 'display' function
- a message rather than a warning is now issued when displaying multiframe images using the 'raster' method
- range clipping to [0:1] in 'writeImage'

version 3.99.10
- improved 'getFrame' function: better performance by reassigning array dimension only when needed

version 3.99.9
- 'font-face' misspelling in 'display.template'
- restored the original 'getFrame' function

version 3.99.8
- substituted the former GTK+ based 'display' function by the new one relying on 'displayInBrowser' and 'displayRaster' functions
- substituted all calls to 'paste0' by 'paste'
- disabled bilinear filtering of rescaled images in the JavaScript image viewer
- fixed a minor bug in the 'displayRaster' function: a warning message was triggered for single-frame images

version 3.99.7
- changed handling of greyscale images containing an alpha channel (aka. GA): instead of discarding the second channel and reading pixel data into a 'Greyscale' Image both channels are now stored in a 'Color' Image
- removed 'readImageOld' and 'writeImageOld'
- removed 'inst/scripts/newAgainstOld.R'
- updated 'inst/scripts/readWriteTest.R'

version 3.99.5
- new 'displayInBrowser' function: preview of the new JavaScript based image viewer

version 3.99.4
- readImage' can now read directly from URLs
- some fixes and improvements to 'displayRaster'

version 3.99.3
- replaced 'readImage' and 'writeImage' by the new 'readImage2' and 'writeImage2' functions; moved the previous ones to 'readImageOld' and 'writeImageOld'

version 3.99.2
- bumped version from 4.0.1 to 3.99.2 to prepare the future 4.0.0 version
- refactored the functions, not using ImageMagick any longer: translate, affine, rotate, resize
- removed: animate
- deprecated: blur, equalize
- todo: man pages have to be synced with recent changes (blur, resize, affine, rotate, translate, display)
- todo: overhaul the unit tests
- todo: remove the old moment generating functions: hullFeatures...
- todo: remove last dependencies to IM
- fixed a bug in 'erode'/'dilate' functions: incorrect range of loop indices caused memory reads from outside the kernel vector
- added 'readImage2' and 'writeImage2' functions: candidates for replacing the original ImageMagick based I/O functions
- added 'swapXY' function swapping the first two indices of an image array during I/O operations
- added 'displayRaster' function displaying images using R graphics
- modified 'getFrame': improved performance
- modified 'as.raster'
- 'inst/images/lena.gif' is now 'inst/images/lena.png' (preparing for dropping GIF support)
- in '/inst/scripts/': scripts for testing the new read/write functions against the former ones using test images from the on-line EBImage Test Images repository (http://www-huber.embl.de/EBImage/ExampleImages/)

version 3.13.2
- deprecated 'equalize'
- fixed occurences of partial argument matching that 'R CMD check' had complained about

version 3.13.1
- fixed a bug in ImageMagickCall that cause some matrices not to be normalized to [0;1] before IM calls

version 3.13.0
- addition of greyscale functions for computation of the self-complementary top-hat (I. Kats)
- a median filter based on Perreault's constant time median filter (J. Barry)

3.11.2
- fixed the angle computation of computeFeatures.moment (there was a sign inversion before for angles larger than pi/4)

3.9.9
- animate() does not work anymore (IM issues I guess...) and now calls display(); I will reimplement the animating function using timer messages in display()

3.9.8
- fixed flop() when working with rectangular images (bug reported by Takeo Katsuki)

3.9.7
- TrueColor is not present any more
- fixed paintObjects using Kevin Keraudren's bug fix
- paintObjects behavior has now changed with respect to the opacity parameter

3.9.6
- the functions getFeatures, hullFeatures, edgeProfile, edgeFeatures are now obsolete
- the functions moments, cmoments, smoments, rmoments, haralickFeatures, haralickMatrix, zernikeMoments are now obsolete 
- the functions are still exported for backward compatibility reasons
- removed some TrueColor tests, which is going to be discarded from EBImage
- removed the deprecated arguments: iter, no.GTK, main, colorize

3.9.5
- exporting computeFeatures

3.9.4
- fixed haralickFeatures and haralickMatrix when no objects are present

3.9.3
- experimental support for computeFeatures
- ocontour does not return empty objects anymore

3.9.2
- the gaussian shape in makeBrush() is now conform to Matlab (J. Barry)
- added the affine() transform

3.9.1
- added the gaussian shape in makeBrush()
- fixed the quality argument in writeImage()

3.7.1
- added getFrame(), to extract the i-th frame of an image
- from Paul Murrell: added a PROTECT/UNPROTECT statement in lib_readImages()
- from Paul Murrell: added as.raster.Image() 

3.5.5
- now supports Cellomics .c01 image file format

3.5.4
- drawCircle() now returns the transformed image and does not modify the input image anymore 

3.5.3
- removed print click position feature

3.5.2
- added drawCircle()
- display() now prints click positions

3.5.1
- lgomp was removed from linking options, to prevent a segfault caused in OpenSUSE 11.2 and 11.3 by dynamic linking of lgomp (optionally used by ImageMagick but not used in EBImage) together with lpthread (required and used by GTK)
- removed Makevars.in
- minimal IM required version is now 6.3.7
- lower vignette image quality to save space

3.3.2
- now uses MagickCoreGenesis and MagickCoreTerminus to start/terminate ImageMagick, to be compatible with IM 6.6.x

3.3.1
- removed frameDist, matchObject
- removed stopIfNotImage, morphKern, mkball, mkbox
- removed header, assert, chooseImage
- removed resample, sharpen, umask, modulate
- removed negate, affinet, normalize2, noise
- removed mediansmooth, cgamma, enhance, denoise
- removed contrast, despeckle, edge, segment
- removed cthresh, athresh
- removed channelMix
- removed applyGaussian and pseudoZernike

3.1.3 
- merge devel with release version 3.0.1

3.0.1
- updated CHANGES
- updated manual pages
- now uses is(x, 'Image') instead of class(x)=='Image' to allow people inherit from the EBImage class
- updated INSTALL file, with new tips for Windows and MacOS users
- removed Gene*.tif old images

2.99.8
- new INSTALL
- new vignette

2.99.7
- stackObjects OK

2.99.6
- doc: propagate, combine, tile, untile, rmObjects, reenumerate, hullFeatures

2.99.5
- channel OK
- paintObjects, drawtext OK
- colors.c removed
- doc: watershed
- simpler combine

2.99.4
- deprecated channelMix
- doc: filter2, moments, cmoments, smoments, rmoments
- doc: paintObjects, getFeatures, rgbImage, channel

2.99.3
- bwlabel OK
- safer rgbImage

2.99.2
- doc: tresh
- floodFill and fillHull : doc + test + examples

2.99.1
- starting the pre 3.0.0 release
- doc: equalize, blur, gblur, normalize, EBImage, EBImage-deprecated

2.7.22
- fixed a bug preventing from reading palette images in color
- deprecated all ImageMagick functions except blur, gblur, equalize, resize and rotate
- validImage now checks validity of arrays
- new doc for ocontour, translate, resize, rotate , flip, flop
- new examples for makeBrush

2.7.21
- moment features renamed from '*' to 'm.*'
- geometric hull features  from 'h.*' to 'g.*' to not to be confused with Haralick's features 'h.*'
- moment features now need ref to be computed
- getFeatures now just concatenate hull, moments, edge, haralick and zernike features
- no more s2maj and s2min in hullFeatures: now only l1 and l2 (eigenvalues of the covariance matrix)(to be consistent with moments)

2.7.20
- outline renamed in ocontour, ocontour documentation added
- build warnings should disappear

2.7.19
- outline added

2.7.16
- fixed warnings due to unused variables in C code
- fixed a drawtext bug which prevented EBImage to be checked on R 2.9.0
- fixed floodFill example by restoring inst/images/holes.png

2.7.15
- no warnings anymore in R CMD check
- S4 methods removed
- header and assert deprecated
- test framework added
- documentation updated
- morphKern, mkball and mkbox deprecated 
- all '...' arguments removed
- horizontal slider and clean display.c code added
- zernikeMoments arguments 'pseudo' and 'apply.Gaussian' deprecated
- display and readImage argument 'colormode' deprecated
- display arguments: 'main', 'no.GTK' deprecated
- .ImageCall and ensureStorageMode functions removed

2.7.11
- no ImageX object anymore: Image now extends array

2.7.10
- fixed ReadImage bug when filename=''

2.7.9
- created tile.c, tile.h
- out of range [0:1] normalize for Magick
- matrix: channel 4, untile, getFeatures fixed
- x11 channel OK

2.7.8
- validImage in C, removed isImage in C
- merged IndexedImage class within Image, no IndexedImage class anymore !
- removed spurious '...'
- classUnion ImageX instead of Image !
- now Image supports non-numeric storage.mode (e.g. logical) !
- ImageCall instead of Call to check Image validity and storage.mode
- deprecated: matchObject, stopIfNotImage

2.7.7
- reenumerate, hullFeatures, rmObjects, watershed: work fine on md and Color
- watershed: fixed bug when used on distmap(lena>0.5)
- getFeatures, hullFeatures, edgeProfile, edgeFeatures: work fine on md and Color
- cmoments, smoment, rmoments, moments: work fine on md and Color
- haralickFeatures, haralickMatrix, zernikeMoments: work fine on md and Color
- zernikeMoments: work fine on md and Color
- frameDist deprecated
- class.IndexedImage.R: stop message in case of TrueColor now OK
- checked all INTEGER(GET_DIM())[2] OK
- merged all features in features.R
- renamed methods-display.R in display.R, filters_watershed.cpp in watershed.cpp
- watershed is now interruptable
- objects methods moved from class.IndexedImage.R to objects.R

2.7.6
- fixed dy instead of dx in lib_filterThresh L37 in nFramePix = (2 * dx + 1) * (2 * dx + 1); (bug submitted by Glenn Davis)
- tile, untile, thresh: works fine on md, Color
- vignettes build OK
- translate: check param input OK
- keeping correct storage.mode after binary operations on TrueColor images
- deprecated functions moved to deprecated.R
- vignette changes: (indexing a[,,,1] instead of a[,,1] and promote usage of rgbImage)
- unit test inst/scripts/test.R added
- new deprecated.R file

2.7.5
- functions copy, .isCorrectType, .correctType have been removed
- multidimensional arrays are now handled
- new color mode Color added
- functions getNumberOfFrames, translate added
- signature combine has been changed
- validity method added
- file filters.R renamed in magick.R
- file spatial.R added
- abind dependency added
- new fast distmap algorithm, up to 1000 times faster
- readImage now uses by default the native image color mode
- C functions getColorMode, getNumberOfFrames, getNumberOfChannels, getColorStrides added
- C function lib_paintFeatures renamed to paintObjects
- C function lib_matchFeatures renamed to matchObjects
- C function lib_deleteFeatures renamed to rmObjects
- C function lib_stack_objects renamed to stackObjects
- C function lib_tile_stack renamed to tile
- C function lib_untile renamed to untile
- display is faster since pixbuf are now directly built from SEXP
- writeImage now uses a quality of 100 by default
- keep correct storage.mode after binary operations 
- the Image constructor is doing now the conversion between TrueColor and (Grayscale or Color) images
- cleaner show, print methods